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Fwd: Other: Minimum Information about a Phylogenetic Analysis
by Karen Cranston 23 Aug '12

23 Aug '12

(Apologies for cross-posting). Please take some time for the following survey about metadata on evolutionary trees. Your responses will inform both the Minimum Information about a Phylogenetic Analysis (MIAPA) standard and also the metadata collected and used to assemble the Open Tree of Life. Cheers, Karen ---------- Forwarded message ---------- From: <evoldir(a)evol.biology.mcmaster.ca> Date: Thu, Aug 23, 2012 at 4:37 AM Subject: Other: Minimum Information about a Phylogenetic Analysis To: karen.cranston(a)gmail.com What data makes a phylogenetic tree useful? When publishing a phylogenetic tree, or evaluating a tree, we generally want more than simply the tree structure - for example, who inferred the tree? using what data and what methods? what are the organisms at the tips? what are the support values? Of course, those who use / evaluate trees want as much data as possible about a tree. Those who publish / database trees want a quick and simple submission system. How do we balance these sometimes conflicting viewpoints? The following survey asks you to categorize various data elements about trees in terms of 1) how useful is the data? and 2) how difficult is it to collect? The survey should take about 10 minutes. https://duke.qualtrics.com/SE/?SID=SV_b2upIMII4fxJkAA This survey is brought to you by MIAPA and Open Tree of Life. MIAPA (http://www.evoio.org/wiki/MIAPA) aims to develop a formal spec for Minimum Information About a Phylogenetic Analysis. The Open Tree of Life (http://opentreeoflife.org) is collecting input phylogenies for synthesis into a comprehensive tree of life. We will share the results via the MIAPA and Open Tree of Life websites, and results will inform the MIAPA standard as well as the collection trees for Open Tree of Life. If you have any questions about this project, please contact Karen Cranston (karen.cranston(a)nescent.org). Thank you! Karen Cranston (on behalf of MIAPA and Open Tree of Life) National Evolutionary Synthesis Center -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Karen Cranston, PhD Training Coordinator and Informatics Project Manager nescent.org @kcranstn ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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NISO/DCMI Webinar: Metadata for Managing Scientific Research Data
by DCMI Announce 15 Aug '12

15 Aug '12

******** PLEASE EXCUSE THE CROSS-POSTING ******** WEBINAR: NISO/DCMI Webinar: Metadata for Managing Scientific Research Data DATE: August 22, 2012 TIME: 1:00 - 2:30 p.m. (Eastern Time) EVENT WEBPAGE: http://www.niso.org/news/events/2012/dcmi/scientific_data/ ABOUT THE WEBINAR The past few years have seen increased attention to national and international policies for data archiving and sharing. Chief motivators include the proliferation of digital data and a growing interest in research data and supplemental information as a part of the framework for scholarly communication. Key objectives include not only preservation of scientific research data, but making data accessible to verify research findings and support the reuse and repurposing of data. Metadata figures prominently in these undertakings, and is critical for the success of any data repositories or archiving initiative, hence increased attention to metadata for scientific data -- specifically for metadata standards development and interoperability, data curation and metadata generation processes, data identifiers, name authority control (for scientists), Linked Data, ontology and vocabulary work, and data citation standards. This NISO/DCMI webinar will provide a historical perspective and an overview of current metadata practices for managing scientific data, with examples drawn from operational repositories and community-driven data science initiatives. It will discuss challenges and potential solutions for metadata generation, identifiers, name authority control, Linked Data, and data citation. SPEAKERS Jane Greenberg, professor at the School of Information and Library Science (SILS) at the University of North Carolina at Chapel Hill and director of the SILS Metadata Research Center, is well known for research and writing on topics ranging from automatic metadata creation to metadata best practices, ontology research, Semantic Web, data repositories, thesauri, and scientific data curation. She has served as Principal Investigator or partner on a number of grants from the Institute of Museum and Library Services, National Science Foundation, and the National Institute of Health, and actively participates in organizations such as the American Library Association, American Society for Information Science and Technology, and the Dublin Core Metadata Initiative. Jane is the recipient of the 2012 Margaret Mann Citation from the Association for Library Collections & Technical Services (ALCTS). Thomas Baker, Chief Information Officer of the Dublin Core Metadata Initiative, has recently co-chaired the W3C Semantic Web Deployment Working Group and the W3C Incubator Group on Library Linked Data. REGISTRATION Registration is per site (access for one computer) and closes at 12:00 pm Eastern on August 22, 2012. Discounts are available for NISO and DCMI members and students. Can’t make it on the webinar date/time? Register now and gain access to the recorded archive for one year. Visit the event webpage to register and for more information: http://www.niso.org/news/events/2012/dcmi/scientific_data/

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DC-2012 in Malaysia five weeks away
by DCMI Announce 26 Jul '12

26 Jul '12

DC-2012 in Kuching, Sarawak, Malasia is a little over five weeks away. Pre-conference includes two full days of tutorials on the Semantic Web starting on 3 September 2012.[1] Led by Sam Oh and Karen Coyle in day-long sessions, the two tutorials promise to take you from simple data to Linked Data. The three-day conference begins on Wednesday, 5 September and includes an exciting program of peer reviewed papers, project reports and posters.[2] DC-2012 keynote speakers Dan Brickley and Karen Coyle [3] join four other keynotes in the collocated meetings of Knowledge Technology Week 2012.[4] So, join us in beautiful Malaysia. Registration is open.[5] [1] http://dcevents.dublincore.org/index.php/IntConf/index/pages/view/tutorials… [2] http://dcevents.dublincore.org/index.php/IntConf/index/pages/view/program-2… [3] http://dcevents.dublincore.org/index.php/IntConf/index/pages/view/speakers-… [4] http://ktw.mimos.my/ktw2012/ [5] http://ktw.mimos.my/info/index.html

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Public Participation in Digitization of Biodiversity Specimens Workshop
by Austin Mast 22 Jun '12

22 Jun '12

It is our pleasure to announce that iDigBio, the National Science Foundation’s National Resource for Advancing Digitization of Biological Collections (www.idigbio.org), is offering a workshop focused on engaging the public in the digitization of the US's ca. 1 billion biodiversity specimens in ways that are interesting and educational for the participants and efficient and reliable for the projects managing the digitization. The workshop is co-organized by iDigBio’s Public Participation in Digitization Working Group and iDigBio’s Education and Outreach Working Group. The target audience for the workshop includes digitization project leaders, biodiversity informatics software developers, and informal education community members. The workshop will (1) identify steps in the digitization process that could involve the public, (2) establish one or more workflows for each of those steps, keeping the motivations driving public participants and digitizing institutions in mind, (3) identify existing tools, expertise, and communities that can be engaged in the workflows and gaps where new tools, expertise, or communities are needed, and (4) start individuals or small groups on the path of making those workflows a reality. The workshop will be held at University of Florida in Gainesville, Florida, September 28–29, 2012. Funding is available to support travel and per diem for five additional participants through a competitive application process. Those desiring to attend this workshop should submit their CV and a succinct paragraph (<200 words) explaining how their attendance will contribute to the successful completion of the four workshop goals given above to Cathy Bester (cbester(a)flmnh.ufl.edu) by July 16, 2012 The committee anticipates notifying applicants of decisions by July 20. Questions about the content of the workshop can be directed to Austin Mast (amast(a)bio.fsu.edu). With best regards, Austin Mast (on behalf of the iDigBio Public Participation in Digitization Working Group) and Betty Dunckel (on behalf of the iDigBio Education and Outreach Working Group) Austin Mast Associate Professor Director of the Robert K. Godfrey Herbarium Member of the Steering Committee of iDigBio, The National Resource for Advancing Digitization of Biological Collections Department of Biological Science 319 Stadium Drive Florida State University Tallahassee, FL 32306-4295 U.S.A. Office: King Life Science Building, room 4065 Lab: King Life Science Building, rooms 4068 and 4084 Herbarium: Biological Science Unit One, room 100 Voice: 1 (850) 645-1500 Fax: 1 (850) 645-8447 amast(a)bio.fsu.edu

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Biodiversity Informatics White Paper: first draft
by Dave Roberts 15 Jun '12

15 Jun '12

Dear all, we have drawn together the initial ideas and contributions people have made into a first draft here: http://is.gd/WhitePaperChapters The format we've chosen to use follows the LERU report (link is on the first page of the Googledoc) which pitches a bullet point followed by a supporting paragraph. Inevitably this is too short to take much of the argument made in some contributions. I suggest that people can either tidy up their chapters and we bundle them in an annex or I'll try and edit them from notes into English and keep them as available. Note also the details of the public meeting in Brussels on 17th July. Details on the Googledoc. Please modify the document directly, but log into Google or otherwise identify yourself so that we can add you to Annex 1 (list of contributors). Cheers, Dave Roberts -- Dr D.McL. Roberts, Tel: +44 (0)20 7942 5086 Dept. Zoology, Fax: +44 (0)20 7942 5054 The Natural History Museum, Cromwell Road, London SW7 5BD Great Britain Email: dmr at nomencurator dot org Web page: http://scratchpads.eu http://www.nhm.ac.uk/research-curation/projects/euk-extreme/ -- "Researchers typically build databases the quickest way they know how, without necessarily considering whether they will work with other databases." Heidi Ledford, Nature 25 June 09, p1048. --

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Last reminder: Deadline for iEvoBio Challenge Competitions is approaching
by Cellinese,Nico 12 Jun '12

12 Jun '12

The deadline for submissions to the yearly iEvoBio Challenge is June 25, 2012, and is rapidly approaching! This is our last reminder. This year’s theme is "Synthesizing Phylogenies," and further information on criteria for challenge entries, how to submit them, and award amount can be found at http://ievobio.org/challenge.html. Also, Biomatters Ltd is running the Geneious Challenge alongside iEvoBio’s competition. The goal of this challenge is to develop a new and exciting visualization or analysis plugin to Geneious Pro, using the public API. Seehttp://ievobio.org/geneious_challenge.html for more information. The deadline for this competition is also June 25. More details about the iEvoBio conference and program are available at http://ievobio.org<http://ievobio.org/>. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Society of Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign

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TDWG Executive Committee Venue Decision
by Chuck Miller 16 May '12

16 May '12

To TDWG Members: The Executive Committee has been requested to comment regarding its decision to hold this year’s meeting in Beijing, China. Its Constitution establishes Biodiversity Information Standards (TDWG) as “a not-for-profit, scientific and educational association formed to establish international collaboration among the creators, managers and users of biodiversity information so as to promote the wider and more effective dissemination of information about the world's heritage of biological organisms for the benefit of the world at large.” The Executive Committee’s decision to host the 2012 meeting in China was based on several factors: 1) A desire to more evenly spread the travel hardship and costs of the meeting around the globe over time, 2) A desire to enable attendees who otherwise would not have the resources to travel internationally,, 3) The Chinese Academy of Science’s offer to host the meeting in 2012, 4) Recent advances in biodiversity informatics in China (e.g. Catalogue of Life, Encyclopedia of Life), and 5) Interest in expanding “international collaboration” and “wider and more effective dissemination of information” through direct contact with the Chinese biodiversity informatics community in their local region, as has been done in other regions of the world in the past. The Executive Committee therefore decided last year to welcome the offer from the Chinese Academy of Sciences, which now expects at least 50 local attendees at this year’s meeting, the largest participation of Asian scientists in the history of TDWG meetings. Objections to holding the meeting in China have cited politically based reasons: “routine governmental suppression of internet connectivity on political grounds.” TDWG is a scientific and educational association, not a political one. TDWG comprises a global membership. Locating a TDWG meeting in a particular country does not imply an endorsement of that country's policies; it is instead an expression of TDWG’s purpose to collaborate to widely disseminate information for the benefit of the world at large. Further, there is no part of TDWG’s constitution, mission or purpose that implies or endorses isolationist, discriminatory, or punitive actions of any kind against anyone, any organization or any political entity. We look forward to your support to make this another successful and informative annual meeting and the opportunity to exchange cultures in an atmosphere of mutual respect and a common desire to make the world a better place for ourselves and future generations. Best regards, Chuck Miller, on behalf of the TDWG Executive Committee Chair Biodiversity Information Standards (TDWG)

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Re: [tdwg] tdwg 2012 in inappropriate venue
by Annie Simpson 11 May '12

11 May '12

Dear Fellow TDWG members: Often the discussions on TDWG lists can overwhelm due to number of responses and depth of content. I am therefore astounded that there have been no replies to Bob Morris' well-thought-out and convincingly-delivered argument of 22-April (copied here below) about our 2012 meetings. I did not answer sooner under the assumption that there was discussion going on behind the scenes by the TDWG Executive. So far, crickets. I'd like to go on the record with a personal but hesitant response that does not reflect the views of my employer. I share Bob's concerns. What do the rest of you think? Annie Simpson From: Bob Morris <morris.bob(a)gmail.com> To: tdwg(a)lists.tdwg.org Date: 22/04/2012 15:22 Subject: [tdwg] tdwg 2012 in inappropriate venue Sent by: tdwg-bounces(a)lists.tdwg.org Dear fellow TDWG members, As I said publicly at TDWG 2011, I feel that it is inappropriate for an organization devoted to the open exchange of scientific data and information to hold a meeting in a country where there is routine governmental suppression of internet connectivity on political grounds. I personally would attend any scientific meeting in such a country except one by an organization like TDWG which should be taking a position about openness of access to information, and I hope others will join me in this position and publicly decline to attend TDWG 2012. Sometimes an argument is made in such cases that participation is a way to support the hosting organization, which in this case is eminent. But often just the opposite can result: the authorities will proudly say to themselves: "See, they come anyway." Bob Morris -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Harvard University Herbaria Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram === The content of this communication is made entirely on my own behalf and in no way should be deemed to express official positions of The University of Massachusetts at Boston or Harvard University. _______________________________________________ tdwg mailing list tdwg(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg

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Call for Challenge entries for iEvoBio conference
by Cellinese,Nico 10 May '12

10 May '12

Many trees enter. Fresh analysis ensues. New insights emerge. As a reminder, the iEvoBio conference is again holding a Challenge competition in 2012, this time on the theme, "Synthesizing Phylogenies." Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website at http://ievobio.org/challenge.html. Submissions are due by June 25, 2012. Cash prizes will be awarded for first place (USD 1,500) and runner-up entries. The winning entries will be selected by a vote of the iEvoBio meeting participants. Also, alongside the iEvoBio Challenge, 2012 iEvoBio sponsor Biomatters Ltd is running the Geneious Challenge. The goal of this challenge is to develop a new plugin to Geneious Pro, using the public API, that enables a new and exciting visualization or analysis. The winning entry will receive a $1000 cash prize, and all entrants who submit by the deadline will receive a 12-month subscription license. The deadline for the Geneious Challenge is the same as for the iEvoBio Challenge. Seehttp://ievobio.org/geneious_challenge.html for more information. More details about the iEvoBio conference and program are available at http://ievobio.org<http://ievobio.org/>. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign

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Job: NESCent User Interface Design and Web Application Developer
by Kristen Eisenberg 03 May '12

03 May '12

The National Evolutionary Synthesis Center (NESCent) seeks a creative and enthusiastic individual to design user interfaces and web applications for scientific applications. The incumbent will work as part of a small informatics team in close collaboration with domain scientists. NESCent (http://nescent.org) is an NSF-funded center dedicated to cross-disciplinary research in evolutionary science. Our informatics team works closely with visiting and resident scientists to support their custom software and database development needs. All NESCent software products are open-source, and the Center has a number of initiatives to actively promote collaborative development of community software resources (http://informatics.nescent.org). Above all, we are enthusiastic about our work, about the mission of the Center, and about the contribution of informatics to that mission. Kristen Eisenberg Billige Flüge Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: utebachmeier at gmail.com Site: http://flug.airego.de - Billige Flüge vergleichen

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